Much of cancer research over the past 50 years has been devoted to the analyses of genes that are expressed differently in tumor cells compared to their normal counterparts. Although hundreds of studies have pointed out differences in the expression of one or a few genes, no comprehensive study of gene expression in the cancer cell has been reported. It is therefore not known how many genes are expressed differentially in tumor versus normal cells, whether the bulk of these differences are cell autonomous rather than being dependent on the tumor microenvironment, and whether most differences are cell-type specific or tumor specific. Thus there is a need in the art for information on the molecular changes that occur in cells during cancer development and progression.